A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils
BackgroundSoil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-i...
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ftcdlib:oai:escholarship.org:ark:/13030/qt4kn746f2 2023-10-01T03:51:56+02:00 A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van De Peer, Yves Cowan, Don A Makhalanyane, Thulani P 40 2018-12-01 application/pdf https://escholarship.org/uc/item/4kn746f2 unknown eScholarship, University of California qt4kn746f2 https://escholarship.org/uc/item/4kn746f2 public Microbiome, vol 6, iss 1 Genetics Infectious Diseases Antimicrobial Resistance Infection Life Below Water Antarctic Regions Anti-Bacterial Agents Bacteria Drug Resistance Multiple Bacterial Gene Transfer Horizontal Genes Membrane Transport Proteins Metagenomics Soil Microbiology Antibiotic resistance genes Soil resistome Antarctica Ecology Microbiology Medical Microbiology article 2018 ftcdlib 2023-09-04T18:04:53Z BackgroundSoil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity.MethodsWe used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs.ResultsIn total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = - 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events.ConclusionsARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments. Article in Journal/Newspaper Antarc* Antarctic Antarctica University of California: eScholarship Antarctic Mackay ENVELOPE(168.517,168.517,-77.700,-77.700) Mackay Glacier ENVELOPE(162.000,162.000,-76.967,-76.967) |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Genetics Infectious Diseases Antimicrobial Resistance Infection Life Below Water Antarctic Regions Anti-Bacterial Agents Bacteria Drug Resistance Multiple Bacterial Gene Transfer Horizontal Genes Membrane Transport Proteins Metagenomics Soil Microbiology Antibiotic resistance genes Soil resistome Antarctica Ecology Microbiology Medical Microbiology |
spellingShingle |
Genetics Infectious Diseases Antimicrobial Resistance Infection Life Below Water Antarctic Regions Anti-Bacterial Agents Bacteria Drug Resistance Multiple Bacterial Gene Transfer Horizontal Genes Membrane Transport Proteins Metagenomics Soil Microbiology Antibiotic resistance genes Soil resistome Antarctica Ecology Microbiology Medical Microbiology Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van De Peer, Yves Cowan, Don A Makhalanyane, Thulani P A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils |
topic_facet |
Genetics Infectious Diseases Antimicrobial Resistance Infection Life Below Water Antarctic Regions Anti-Bacterial Agents Bacteria Drug Resistance Multiple Bacterial Gene Transfer Horizontal Genes Membrane Transport Proteins Metagenomics Soil Microbiology Antibiotic resistance genes Soil resistome Antarctica Ecology Microbiology Medical Microbiology |
description |
BackgroundSoil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity.MethodsWe used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs.ResultsIn total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = - 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events.ConclusionsARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments. |
format |
Article in Journal/Newspaper |
author |
Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van De Peer, Yves Cowan, Don A Makhalanyane, Thulani P |
author_facet |
Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van De Peer, Yves Cowan, Don A Makhalanyane, Thulani P |
author_sort |
Van Goethem, Marc W |
title |
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils |
title_short |
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils |
title_full |
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils |
title_fullStr |
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils |
title_full_unstemmed |
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils |
title_sort |
reservoir of ‘historical’ antibiotic resistance genes in remote pristine antarctic soils |
publisher |
eScholarship, University of California |
publishDate |
2018 |
url |
https://escholarship.org/uc/item/4kn746f2 |
op_coverage |
40 |
long_lat |
ENVELOPE(168.517,168.517,-77.700,-77.700) ENVELOPE(162.000,162.000,-76.967,-76.967) |
geographic |
Antarctic Mackay Mackay Glacier |
geographic_facet |
Antarctic Mackay Mackay Glacier |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
Microbiome, vol 6, iss 1 |
op_relation |
qt4kn746f2 https://escholarship.org/uc/item/4kn746f2 |
op_rights |
public |
_version_ |
1778517302284648448 |